rs2633306

Positions:

• chr10-73892689-A-C
• chr10-73892689-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.701 in 152,084 control chromosomes in the GnomAD database, including 37,992 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (37992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106506 AN: 151964 Hom.: 37968 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.701 AC: 106568 AN: 152084 Hom.: 37992 Cov.: 32 AF XY: 0.691 AC XY: 51375 AN XY: 74322

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.746

Alfa AF: 0.675 Hom.: 10027

Bravo AF: 0.700

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2633306; hg19: chr10-75652447;